Contacts of the strand formed by residues 99 - 109 (chain B) in PDB entry 3F5O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B GLU* 4.7 6.3 - - - +
42B MET 3.5 4.9 - - - +
43B LYS* 3.4 40.1 + - - +
97B GLY 4.4 0.7 - - - +
98B GLU* 1.3 74.6 - - - +
100B ILE* 1.3 62.9 + - - +
122B ASN* 3.8 7.2 + - - +
123B LYS* 2.9 55.0 + - + +
124B ALA 4.6 0.6 + - - +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLU* 3.1 8.5 - - - +
42B MET* 2.8 69.9 + - + +
44B VAL* 4.0 19.7 - - + -
55B LEU* 4.3 6.7 - - + -
63B LEU* 3.8 19.1 - - + -
94B ALA* 4.2 5.6 - - + -
98B GLU* 4.4 3.1 - - + +
99B ASP* 1.3 77.7 - - - +
101B VAL* 1.3 63.1 + - - +
102B ILE* 3.9 13.5 - - + -
120B LEU* 4.2 12.1 - - + -
121B THR 3.3 8.5 - - - +
122B ASN* 5.1 0.4 - - - -
123B LYS* 4.9 0.4 - - - -
129B ILE* 3.5 25.4 - - + -
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 6.2 0.4 - - + -
39B ILE* 3.7 26.2 - - + -
40B CYS 3.5 3.6 - - - +
41B GLU* 4.4 7.9 - - + +
100B ILE* 1.3 76.2 - - - +
102B ILE* 1.3 63.0 + - - +
103B THR* 3.9 10.9 + - - +
119B ASP 3.5 1.7 - - - +
120B LEU* 3.3 4.0 - - - -
121B THR* 2.8 47.4 + - - +
123B LYS* 3.9 36.1 - - + -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 5.4 0.7 - - + -
38B VAL 3.7 1.6 - - - +
39B ILE* 3.3 3.6 - - - -
40B CYS* 2.8 53.0 + - + +
41B GLU* 4.1 7.4 - - - -
42B MET* 4.3 4.7 - - + +
63B LEU* 4.1 23.8 - - + +
67B ILE* 3.9 26.9 - - + +
100B ILE* 3.9 28.3 - - + +
101B VAL* 1.3 73.7 - - - +
103B THR* 1.3 59.2 + - - +
104B ALA 4.1 0.2 + - - -
118B VAL* 3.4 28.7 - - + -
119B ASP 3.3 3.6 - - - +
120B LEU* 3.9 25.8 - - + -
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LYS* 3.7 31.0 - - - +
38B VAL 3.5 2.9 - - - +
39B ILE* 4.0 13.4 - - + +
101B VAL* 3.9 15.4 + - - +
102B ILE* 1.3 75.2 + - - +
104B ALA* 1.3 64.7 + - - +
105B HIS* 5.2 7.4 + - - +
117B SER 3.8 0.7 - - - +
118B VAL* 3.2 4.6 - - - -
119B ASP* 2.8 47.4 + - + +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LYS* 3.3 5.5 - - - +
38B VAL 2.8 34.4 + - - +
67B ILE* 3.4 42.4 - - + +
68B SER* 3.7 11.9 - - - +
71B ALA* 4.0 4.8 - - + +
102B ILE 4.1 0.8 - - - -
103B THR* 1.3 75.4 - - - +
105B HIS* 1.3 63.5 + - - +
117B SER 3.3 4.0 - - - -
118B VAL* 3.8 9.0 - - + -
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY 3.3 8.5 - - - +
37B LYS* 4.2 17.7 - - + -
71B ALA* 4.6 0.9 - - - -
103B THR* 5.2 7.0 + - + +
104B ALA* 1.3 76.9 - - - +
106B VAL* 1.3 71.7 + - - +
107B LEU* 3.2 25.8 + - + +
116B THR* 3.2 5.1 - - - -
117B SER* 2.6 64.7 + - - -
119B ASP* 6.5 0.7 - - - -
131C GLN* 5.7 1.1 - - - -
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY* 2.8 27.9 + - - +
71B ALA* 3.8 24.5 - - + +
72B LEU* 3.7 24.0 - - + -
75B THR* 4.0 5.8 - - + -
105B HIS* 1.3 80.0 - - - +
107B LEU* 1.3 63.0 + - - +
108B LYS* 3.8 11.0 - - - +
109B GLN* 3.7 28.7 - - + +
115B PHE 3.7 8.5 - - - +
116B THR* 4.2 3.1 - - + -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B HIS* 3.2 33.2 - - + +
106B VAL* 1.3 74.0 - - - +
108B LYS* 1.3 59.6 + - - +
115B PHE* 2.8 14.8 + - + +
116B THR 4.1 10.3 - - - +
117B SER* 3.9 20.0 - - - +
133B ARG* 4.1 10.3 - - - -
91C MET* 3.7 27.6 - - + -
128C LEU* 4.0 25.7 - - + +
131C GLN* 3.9 30.7 - - - +
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B VAL* 3.6 3.8 - - - +
107B LEU* 1.3 81.6 - - - +
109B GLN* 1.3 83.8 + - - +
110B GLY* 3.9 2.2 - - - -
114B ALA* 3.4 1.9 - - - -
115B PHE* 2.9 52.6 + - + +
91C MET* 3.1 38.8 - - + +
92C SER* 4.9 7.4 - - - -
128C LEU* 5.6 3.4 - - + +
150D COA 3.0 32.7 + - - -
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 4.3 9.0 - - + +
75B THR* 3.1 37.6 + - - +
77B ARG* 4.3 18.9 + - - +
79B ALA 5.3 3.0 + - - -
106B VAL* 3.7 22.4 - - + +
108B LYS* 1.3 87.5 + - - +
110B GLY* 1.3 57.8 + - - +
113B LEU 3.7 3.4 - - - -
114B ALA* 4.2 6.1 - - + -
138B LEU* 3.6 27.3 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il